setwd("~/Postgrad/Honours")
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(survival)

Load cohort data:

load('brca2116_dataset.RData')

Two objects:

HIgh or low IQSEC2 include ER+ and ER- samples:

sampleDatap = sampleData[(sampleData$ER.status=="ER+" & sampleData$EndocrineTrt==1) ,]
sampleDatan = sampleData[(sampleData$ER.status=="ER-" & sampleData$PgR.status=="PgR-" & sampleData$EndocrineTrt==1),]

dim(sampleData[sampleData$ER.status=="ER-" & sampleData$PgR.status=="PgR-",])
## [1] 630  17
sampleDataop = filter(sampleDatap, rowSums(is.na(sampleDatap)) != ncol(sampleDatap))
sampleDataon = filter(sampleDatan, rowSums(is.na(sampleDatan)) != ncol(sampleDatan))
expDatop = expDat[,sampleDataop$sampleNames]
expDaton = expDat[,sampleDataon$sampleNames]
IQSEC2pif = ifelse( expDatop["IQSEC2",] > mean(expDatop["IQSEC2",]), 1, 0)
table(IQSEC2pif)
## IQSEC2pif
##   0   1 
## 439 352
plot( survfit( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~ IQSEC2pif ),
xlab = "Time in months", ylab = "Metastasis-free survival", col = c(2,4))
legend('topright', c("IQSEC2 high", "IQSEC2 low"), fill = c('red', 'blue'))

survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~IQSEC2pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~ 
##     IQSEC2pif)
## 
## n=582, 209 observations deleted due to missingness.
## 
##               N Observed Expected (O-E)^2/E (O-E)^2/V
## IQSEC2pif=0 315       73     84.2      1.48      3.39
## IQSEC2pif=1 267       77     65.8      1.89      3.39
## 
##  Chisq= 3.4  on 1 degrees of freedom, p= 0.07
IQSEC2nif = ifelse( expDaton["IQSEC2",] > mean(expDaton["IQSEC2",]), 1, 0)
table(IQSEC2nif)
## IQSEC2nif
##  0  1 
## 19 23
plot( survfit( Surv(sampleDataon$dmfsTime, sampleDataon$dmfsEvent) ~ IQSEC2nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("IQSEC2 high", "IQSEC2 low"), fill = c('red', 'blue'))

for (i in 1:15){
boxplot(expDatop["IQSEC2",i])
}

CDpif = ifelse( expDatop["CD163",] > median(expDatop["CD163",]), 1, 0)
table(CDpif)
## CDpif
##   0   1 
## 398 393
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ CDpif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("CD163 high", "CD163 low"), fill = c('red', 'blue'))

survdiff( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~CDpif )
## Call:
## survdiff(formula = Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ 
##     CDpif)
## 
## n=773, 18 observations deleted due to missingness.
## 
##           N Observed Expected (O-E)^2/E (O-E)^2/V
## CDpif=0 388       81     84.6     0.152     0.301
## CDpif=1 385       92     88.4     0.146     0.301
## 
##  Chisq= 0.3  on 1 degrees of freedom, p= 0.6
CDnif = ifelse( expDaton["CD163",] > median(expDaton["CD163",]), 1, 0)
table(CDnif)
## CDnif
##  0  1 
## 21 21
plot( survfit( Surv(sampleDataon$dmfsTime, sampleDataon$dmfsEvent) ~ CDnif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("CD high", "CD low"), fill = c('red', 'blue'))

HIST1H2AJpif = ifelse( expDatop["HIST1H2AJ",] > mean(expDatop["HIST1H2AJ",]), 1, 0)
table(HIST1H2AJpif)
## HIST1H2AJpif
##   0   1 
## 424 367
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dfsEvent) ~ HIST1H2AJpif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("HIST1H2AJ high", "HIST1H2AJ low"), fill = c('red', 'blue'))

HIST1H2AJnif = ifelse( expDaton["HIST1H2AJ",] > mean(expDaton["HIST1H2AJ",]), 1, 0)
table(HIST1H2AJnif)
## HIST1H2AJnif
##  0  1 
## 23 19
plot( survfit( Surv(sampleDataon$dfsTime, sampleDataon$dfsEvent) ~ HIST1H2AJnif ),
xlab = "Time in months", ylab = "Recurrence-free survival proportion", col = c(2,4))
legend('topright', c("HIST1H2AJ high", "HIST1H2AJ low"), fill = c('red', 'blue'))

survdiff( Surv(sampleDataon$dfsTime, sampleDataon$dfsEvent) ~HIST1H2AJnif )
## Call:
## survdiff(formula = Surv(sampleDataon$dfsTime, sampleDataon$dfsEvent) ~ 
##     HIST1H2AJnif)
## 
## n=25, 17 observations deleted due to missingness.
## 
##                 N Observed Expected (O-E)^2/E (O-E)^2/V
## HIST1H2AJnif=0 15        4     6.34     0.864      2.38
## HIST1H2AJnif=1 10        6     3.66     1.497      2.38
## 
##  Chisq= 2.4  on 1 degrees of freedom, p= 0.1
CXCL13pif = ifelse( expDatop["CXCL13",] > mean(expDatop["CXCL13",]), 1, 0)
table(CXCL13pif)
## CXCL13pif
##   0   1 
## 500 291
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ CXCL13pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CXCL13 high", "CXCL13 low"), fill = c('red', 'blue'))

CXCL13nif = ifelse( expDaton["CXCL13",] > mean(expDaton["CXCL13",]), 1, 0)
table(CXCL13nif)
## CXCL13nif
##  0  1 
## 18 24
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ CXCL13nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CXCL13 high", "CXCL13 low"), fill = c('red', 'blue'))

CXCL13nif
##   GSM79117   GSM79148   GSM79191   GSM79195   GSM79239   GSM79259   GSM79274 
##          1          1          1          1          1          0          0 
##   GSM79292   GSM79341   GSM79351  GSM107082  GSM107131  GSM107166  GSM107183 
##          1          1          1          1          1          0          1 
##    OXF5431    OXF5432    OXF5440    OXF5444    OXF5448    OXF5451    OXF5460 
##          0          0          0          0          1          0          1 
##    OXF5466   GSM50045   GSM50048   GSM50054   GSM50060   GSM50061   GSM50066 
##          1          0          0          1          1          1          0 
##   GSM50071   GSM50093   GSM50116 1639356696 1639355859 1639356632 1639357580 
##          0          0          0          0          1          1          1 
## 1639355773 1639357556 1639356846 1639358104 1639355985 1639356292 1639357162 
##          0          1          1          1          1          0          0
STX8pif = ifelse( expDatop["STX8",] > mean(expDatop["STX8",]), 1, 0)
table(STX8pif)
## STX8pif
##   0   1 
## 393 398
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ STX8pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("STX8 high", "STX8 low"), fill = c('red', 'blue'))

survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~STX8pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~ 
##     STX8pif)
## 
## n=582, 209 observations deleted due to missingness.
## 
##             N Observed Expected (O-E)^2/E (O-E)^2/V
## STX8pif=0 287       78     74.4     0.177     0.352
## STX8pif=1 295       72     75.6     0.174     0.352
## 
##  Chisq= 0.4  on 1 degrees of freedom, p= 0.6
STX8nif = ifelse( expDaton["STX8",] > mean(expDaton["STX8",]), 1, 0)
table(STX8nif)
## STX8nif
##  0  1 
## 22 20
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ STX8nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("STX8 high", "STX8 low"), fill = c('red', 'blue'))

TIMM22pif = ifelse( expDatop["TIMM22",] > mean(expDatop["TIMM22",]), 1, 0)
table(TIMM22pif)
## TIMM22pif
##   0   1 
## 420 371
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ TIMM22pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("TIMM22 high", "TIMM22 low"), fill = c('red', 'blue'))

survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~TIMM22pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~ 
##     TIMM22pif)
## 
## n=582, 209 observations deleted due to missingness.
## 
##               N Observed Expected (O-E)^2/E (O-E)^2/V
## TIMM22pif=0 311       84     78.7     0.360     0.759
## TIMM22pif=1 271       66     71.3     0.397     0.759
## 
##  Chisq= 0.8  on 1 degrees of freedom, p= 0.4
TIMM22nif = ifelse( expDaton["TIMM22",] > mean(expDaton["TIMM22",]), 1, 0)
table(TIMM22nif)
## TIMM22nif
##  0  1 
## 25 17
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ TIMM22nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("TIMM22 high", "TIM22 low"), fill = c('red', 'blue'))

ARHGEF7pif = ifelse( expDatop["ARHGEF7",] > mean(expDatop["ARHGEF7",]), 1, 0)
table(ARHGEF7pif)
## ARHGEF7pif
##   0   1 
## 378 413
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ ARHGEF7pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("ARHGEF7 high", "ARHGEF7 low"), fill = c('red', 'blue'))

survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~ARHGEF7pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~ 
##     ARHGEF7pif)
## 
## n=582, 209 observations deleted due to missingness.
## 
##                N Observed Expected (O-E)^2/E (O-E)^2/V
## ARHGEF7pif=0 273       77       66      1.82      3.27
## ARHGEF7pif=1 309       73       84      1.43      3.27
## 
##  Chisq= 3.3  on 1 degrees of freedom, p= 0.07
ARHGEF7nif = ifelse( expDaton["ARHGEF7",] > mean(expDaton["ARHGEF7",]), 1, 0)
table(ARHGEF7nif)
## ARHGEF7nif
##  0  1 
## 19 23
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ ARHGEF7nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("ARHGEF7 high", "ARHGEF7 low"), fill = c('red', 'blue'))

MKRN2pif = ifelse( expDatop["MKRN2",] > mean(expDatop["MKRN2",]), 1, 0)
table(MKRN2pif)
## MKRN2pif
##   0   1 
## 410 381
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ MKRN2pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("MKRN2 high", "MKRN2 low"), fill = c('red', 'blue'))

survdiff( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~MKRN2pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ 
##     MKRN2pif)
## 
## n=773, 18 observations deleted due to missingness.
## 
##              N Observed Expected (O-E)^2/E (O-E)^2/V
## MKRN2pif=0 402       75     90.2      2.56      5.35
## MKRN2pif=1 371       98     82.8      2.78      5.35
## 
##  Chisq= 5.3  on 1 degrees of freedom, p= 0.02
MKRN2nif = ifelse( expDaton["MKRN2",] > mean(expDaton["MKRN2",]), 1, 0)
table(MKRN2nif)
## MKRN2nif
##  0  1 
## 25 17
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ MKRN2nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("MKRN2 high", "MKRN2 low"), fill = c('red', 'blue'))

PARP3pif = ifelse( expDatop["PARP3",] > mean(expDatop["PARP3",]), 1, 0)
table(PARP3pif)
## PARP3pif
##   0   1 
## 405 386
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ PARP3pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("PARP3 high", "PARP3 low"), fill = c('red', 'blue'))

survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~PARP3pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~ 
##     PARP3pif)
## 
## n=582, 209 observations deleted due to missingness.
## 
##              N Observed Expected (O-E)^2/E (O-E)^2/V
## PARP3pif=0 298       83       75     0.854      1.71
## PARP3pif=1 284       67       75     0.854      1.71
## 
##  Chisq= 1.7  on 1 degrees of freedom, p= 0.2
PARP3nif = ifelse( expDaton["PARP3",] > mean(expDaton["PARP3",]), 1, 0)
table(PARP3nif)
## PARP3nif
##  0  1 
## 18 24
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ PARP3nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("PARP3 high", "PARP3 low"), fill = c('red', 'blue'))

DHRS12pif = ifelse( expDatop["DHRS12",] > mean(expDatop["DHRS12",]), 1, 0)
table(DHRS12pif)
## DHRS12pif
##   0   1 
## 414 377
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ DHRS12pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("DHRS12 high", "DHRS12 low"), fill = c('red', 'blue'))

survdiff( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~DHRS12pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ 
##     DHRS12pif)
## 
## n=773, 18 observations deleted due to missingness.
## 
##               N Observed Expected (O-E)^2/E (O-E)^2/V
## DHRS12pif=0 410       99     90.2     0.851      1.78
## DHRS12pif=1 363       74     82.8     0.928      1.78
## 
##  Chisq= 1.8  on 1 degrees of freedom, p= 0.2
DHRS12nif = ifelse( expDaton["DHRS12",] > mean(expDaton["DHRS12",]), 1, 0)
table(DHRS12nif)
## DHRS12nif
##  0  1 
## 24 18
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ DHRS12nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("DHRS12 high", "DHRS12 low"), fill = c('red', 'blue'))

CXCL13nif
##   GSM79117   GSM79148   GSM79191   GSM79195   GSM79239   GSM79259   GSM79274 
##          1          1          1          1          1          0          0 
##   GSM79292   GSM79341   GSM79351  GSM107082  GSM107131  GSM107166  GSM107183 
##          1          1          1          1          1          0          1 
##    OXF5431    OXF5432    OXF5440    OXF5444    OXF5448    OXF5451    OXF5460 
##          0          0          0          0          1          0          1 
##    OXF5466   GSM50045   GSM50048   GSM50054   GSM50060   GSM50061   GSM50066 
##          1          0          0          1          1          1          0 
##   GSM50071   GSM50093   GSM50116 1639356696 1639355859 1639356632 1639357580 
##          0          0          0          0          1          1          1 
## 1639355773 1639357556 1639356846 1639358104 1639355985 1639356292 1639357162 
##          0          1          1          1          1          0          0
FBXO34pif = ifelse( expDatop["FBXO34",] > mean(expDatop["FBXO34",]), 1, 0)
table(FBXO34pif)
## FBXO34pif
##   0   1 
## 388 403
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ FBXO34pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("FBXO34 high", "FBXO34 low"), fill = c('red', 'blue'))

survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~FBXO34pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~ 
##     FBXO34pif)
## 
## n=582, 209 observations deleted due to missingness.
## 
##               N Observed Expected (O-E)^2/E (O-E)^2/V
## FBXO34pif=0 289       70     76.2     0.502      1.02
## FBXO34pif=1 293       80     73.8     0.518      1.02
## 
##  Chisq= 1  on 1 degrees of freedom, p= 0.3
FBXO34nif = ifelse( expDaton["FBXO34",] > mean(expDaton["FBXO34",]), 1, 0)
table(FBXO34nif)
## FBXO34nif
##  0  1 
## 21 21
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ FBXO34nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("FBXO34 high", "FBXO34 low"), fill = c('red', 'blue'))

CXCL13nif
##   GSM79117   GSM79148   GSM79191   GSM79195   GSM79239   GSM79259   GSM79274 
##          1          1          1          1          1          0          0 
##   GSM79292   GSM79341   GSM79351  GSM107082  GSM107131  GSM107166  GSM107183 
##          1          1          1          1          1          0          1 
##    OXF5431    OXF5432    OXF5440    OXF5444    OXF5448    OXF5451    OXF5460 
##          0          0          0          0          1          0          1 
##    OXF5466   GSM50045   GSM50048   GSM50054   GSM50060   GSM50061   GSM50066 
##          1          0          0          1          1          1          0 
##   GSM50071   GSM50093   GSM50116 1639356696 1639355859 1639356632 1639357580 
##          0          0          0          0          1          1          1 
## 1639355773 1639357556 1639356846 1639358104 1639355985 1639356292 1639357162 
##          0          1          1          1          1          0          0
IL21pif = ifelse( expDatop["IL21",] > mean(expDatop["IL21",]), 1, 0)
table(IL21pif)
## IL21pif
##   0   1 
## 430 361
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ IL21pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("IL21 high", "IL21 low"), fill = c('red', 'blue'))

IL21nif = ifelse( expDaton["IL21",] > mean(expDaton["IL21",]), 1, 0)
table(IL21nif)
## IL21nif
##  0  1 
## 24 18
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ IL21nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("IL21 high", "IL21 low"), fill = c('red', 'blue'))

CXCL13nif
##   GSM79117   GSM79148   GSM79191   GSM79195   GSM79239   GSM79259   GSM79274 
##          1          1          1          1          1          0          0 
##   GSM79292   GSM79341   GSM79351  GSM107082  GSM107131  GSM107166  GSM107183 
##          1          1          1          1          1          0          1 
##    OXF5431    OXF5432    OXF5440    OXF5444    OXF5448    OXF5451    OXF5460 
##          0          0          0          0          1          0          1 
##    OXF5466   GSM50045   GSM50048   GSM50054   GSM50060   GSM50061   GSM50066 
##          1          0          0          1          1          1          0 
##   GSM50071   GSM50093   GSM50116 1639356696 1639355859 1639356632 1639357580 
##          0          0          0          0          1          1          1 
## 1639355773 1639357556 1639356846 1639358104 1639355985 1639356292 1639357162 
##          0          1          1          1          1          0          0
PTNpif = ifelse( expDatop["PTN",] > mean(expDatop["PTN",]), 1, 0)
table(PTNpif)
## PTNpif
##   0   1 
## 511 280
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ PTNpif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("PTN high", "PTN low"), fill = c('red', 'blue'))

PTNnif = ifelse( expDaton["PTN",] > mean(expDaton["PTN",]), 1, 0)
table(PTNnif)
## PTNnif
##  0  1 
## 31 11
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ PTNnif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("PTN high", "PTN low"), fill = c('red', 'blue'))

SLC4A1pif = ifelse( expDatop["SLC4A1",] > mean(expDatop["SLC4A1",]), 1, 0)
table(SLC4A1pif)
## SLC4A1pif
##   0   1 
## 430 361
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ SLC4A1pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("SLC4A1 high", "SLC4A1 low"), fill = c('red', 'blue'))

SLC4A1nif = ifelse( expDaton["SLC4A1",] > mean(expDaton["SLC4A1",]), 1, 0)
table(SLC4A1nif)
## SLC4A1nif
##  0  1 
## 23 19
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ SLC4A1nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("SLC4A1 high", "SLC4A1 low"), fill = c('red', 'blue'))

MBpif = ifelse( expDatop["MB",] > mean(expDatop["MB",]), 1, 0)
table(MBpif)
## MBpif
##   0   1 
## 411 380
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ MBpif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("MB high", "MB low"), fill = c('red', 'blue'))

MBnif = ifelse( expDaton["MB",] > mean(expDaton["MB",]), 1, 0)
table(MBnif)
## MBnif
##  0  1 
## 24 18
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ MBnif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("MB high", "MB low"), fill = c('red', 'blue'))

KIR2DL4pif = ifelse( expDatop["KIR2DL4",] > mean(expDatop["KIR2DL4",]), 1, 0)
table(KIR2DL4pif)
## KIR2DL4pif
##   0   1 
## 412 379
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ KIR2DL4pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("KIR2DL4 high", "KIR2DL4 low"), fill = c('red', 'blue'))

KIR2DL4nif = ifelse( expDaton["KIR2DL4",] > mean(expDaton["KIR2DL4",]), 1, 0)
table(KIR2DL4nif)
## KIR2DL4nif
##  0  1 
## 22 20
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ KIR2DL4nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("KIR2DL4 high", "KIR2DL4 low"), fill = c('red', 'blue'))

CD247pif = ifelse( expDatop["CD247",] > mean(expDatop["CD247",]), 1, 0)
table(CD247pif)
## CD247pif
##   0   1 
## 477 314
plot( survfit( Surv(sampleDataop$dssTime, sampleDataop$dssEvent) ~ CD247pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CD247 high", "CD247 low"), fill = c('red', 'blue'))

CD247nif = ifelse( expDaton["CD247",] > mean(expDaton["CD247",]), 1, 0)
table(CD247nif)
## CD247nif
##  0  1 
## 23 19
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ CD247nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CD247 high", "CXCL13 low"), fill = c('red', 'blue'))

CREG1pif = ifelse( expDatop["CREG1",] > mean(expDatop["CREG1",]), 1, 0)
table(CREG1pif)
## CREG1pif
##   0   1 
## 367 424
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ CREG1pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CREG1 high", "CREG1 low"), fill = c('red', 'blue'))

CREG1nif = ifelse( expDaton["CREG1",] > mean(expDaton["CREG1",]), 1, 0)
table(CREG1nif)
## CREG1nif
##  0  1 
## 22 20
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ CREG1nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CREG1 high", "CREG1 low"), fill = c('red', 'blue'))

CXCL13nif
##   GSM79117   GSM79148   GSM79191   GSM79195   GSM79239   GSM79259   GSM79274 
##          1          1          1          1          1          0          0 
##   GSM79292   GSM79341   GSM79351  GSM107082  GSM107131  GSM107166  GSM107183 
##          1          1          1          1          1          0          1 
##    OXF5431    OXF5432    OXF5440    OXF5444    OXF5448    OXF5451    OXF5460 
##          0          0          0          0          1          0          1 
##    OXF5466   GSM50045   GSM50048   GSM50054   GSM50060   GSM50061   GSM50066 
##          1          0          0          1          1          1          0 
##   GSM50071   GSM50093   GSM50116 1639356696 1639355859 1639356632 1639357580 
##          0          0          0          0          1          1          1 
## 1639355773 1639357556 1639356846 1639358104 1639355985 1639356292 1639357162 
##          0          1          1          1          1          0          0